phylogeny using 2 alleles per loci data

Question

[Cherry]

Hello everyone,

I want to construct a phylogeny based on fasta sequences. Two sequences which contain two alleles stand for one individual, for example:

>indi_1_allele1
AATTCGC
>indi_1_allele2
ACTTAGC
>indi_2_allele1
ACGTAGC
>indi_2_allele2
ACGTATA
..

Does anyone know how to construct a phylogeny using these kind of data? What software can I use?

Answer 1

[h.mon]

Do you have just one gene? If so, just add the two alleles as:

>sp1
sequence
>sp2_seq1
sequence
>sp2_seq2
sequence
>sp3
sequence
..

You may use any phylogeny recontruction software, such as PhyML, RAxML, PHYLIP, Mega...